Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z802824098 (DNV2_NS5A-x0279)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293.15 | 350 mM Magnesium chloride, 10% PEG 4000, 100 mM MES, pH 6.5 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.42 | 49.19 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 82.543 | α = 90 |
| b = 116.835 | β = 90 |
| c = 148.382 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 2 2 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER2 XE 9M | 2023-08-09 | SINGLE WAVELENGTH | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.92124 | Diamond | I04-1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||
| 1 | 1.66 | 74.17 | 100 | 0.121 | 0.126 | 0.034 | 0.999 | 10.9 | 13.3 | 84731 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 1.66 | 1.69 | 99.4 | 4.709 | 4.948 | 1.507 | 0.318 | 10.7 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 5K5M | 1.66 | 74.3 | 79159 | 4263 | 98.4 | 0.19733 | 0.19572 | 0.2176 | 0.22643 | 0.2407 | RANDOM | 52.463 | ||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
| -2.38 | 0.53 | 1.85 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 30.994 |
| r_dihedral_angle_4_deg | 18.129 |
| r_dihedral_angle_3_deg | 16.403 |
| r_long_range_B_refined | 9.404 |
| r_long_range_B_other | 9.362 |
| r_dihedral_angle_1_deg | 6.432 |
| r_scangle_other | 6.353 |
| r_mcangle_it | 5.746 |
| r_mcangle_other | 5.745 |
| r_scbond_it | 3.949 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4759 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 444 |
| Heterogen Atoms | 75 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| REFMAC5 | refinement |
| Aimless | data scaling |
| PHASER | phasing |
| XDS | data reduction |
